Below are the metadata associated with each sample, as provided by LifeMine.
The table below contains the normalized feature counts per locus ID for each sample.
This is the clustergenes table as provided by LifeMine, which contains the genes and locus IDs from the cluster of interest.
Let’s take a quick look at the distribution of counts for each sample.
The following is a table of the number of expressed genes in each samples, giving a quantititive value to the quality of the expression data. Two thresholds for normalized gene expression were used here: 0.5 and 1.
Shown here are some simple plots of ERCC concentrations after normalization.
This volcano plot shows us a summary view of the differential expression results. Each point on the plot represents one gene in the experiment. Mouse over a point to see a pop-up view with details on the results for that gene. Interactive plots like this are computationally intensive, so we’re only showing here the genes that have a p-value of p <= 0.05.
The y-axis position represents the -log p-value: a higher value indicates that the gene is more significant. The x-axis position shows the log-fold-change for the gene between the engineered and wild-type samples. Genes on the right-hand side of the plot increase in expression in the engineered sample. Genes on the left-hand side decrease in expression in the engineered sample.
The full list of differentially expressed genes can be found in the tables below. Click the “Download” button to view a version of the data in Excel.
| description | |
|---|---|
| symbol | The locus ID of the gene. |
| statistic | The test statistic for this gene. This statistic is an intermediate value used to calculate the p-value. |
| baseMean | The mean expression value across all samples in the analysis. |
| log2FC | The log2-fold-change of gene expression between the engineered strain and wild-type control |
| padj | The p-value for this gene, corrected for multiple testing. |
There are 1 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 12 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 8 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 128 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 7 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
There are 11 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Below are barplots of the normalized read counts for each locus ID within a CDK cluster.
GN003446.00_002768
GN003446.00_003104
GN003446.00_002654
GN003446.00_002608
GN003446.00_002540
GN003446.00_002439
GN003446.00_002333
GN003446.00_002184
GN003446.00_001767
GN003446.00_001767-KO
GN003446.00_002892
GN003446.00_001668
This section includes technical details about the R code used to produce this analysis. Most readers can safely ignore it.
## setting value
## version R version 3.6.0 (2019-04-26)
## os macOS 10.15.5
## system x86_64, darwin17.7.0
## ui unknown
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-07-06
| package | ondiskversion | loadedversion | path | loadedpath | attached | is_base | date | source | md5ok | library | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| acepack | acepack | 1.4.1 | 1.4.1 | /usr/local/lib/R/3.6/site-library/acepack | /usr/local/lib/R/3.6/site-library/acepack | FALSE | FALSE | 2016-10-29 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| annotate | annotate | 1.62.0 | 1.62.0 | /usr/local/lib/R/3.6/site-library/annotate | /usr/local/lib/R/3.6/site-library/annotate | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| AnnotationDbi | AnnotationDbi | 1.46.1 | 1.46.1 | /usr/local/lib/R/3.6/site-library/AnnotationDbi | /usr/local/lib/R/3.6/site-library/AnnotationDbi | TRUE | FALSE | 2019-08-20 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| assertthat | assertthat | 0.2.1 | 0.2.1 | /usr/local/lib/R/3.6/site-library/assertthat | /usr/local/lib/R/3.6/site-library/assertthat | FALSE | FALSE | 2019-03-21 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| backports | backports | 1.1.6 | 1.1.6 | /usr/local/lib/R/3.6/site-library/backports | /usr/local/lib/R/3.6/site-library/backports | FALSE | FALSE | 2020-04-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| base64enc | base64enc | 0.1.3 | 0.1-3 | /usr/local/lib/R/3.6/site-library/base64enc | /usr/local/lib/R/3.6/site-library/base64enc | FALSE | FALSE | 2015-07-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Biobase | Biobase | 2.44.0 | 2.44.0 | /usr/local/lib/R/3.6/site-library/Biobase | /usr/local/lib/R/3.6/site-library/Biobase | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| BiocGenerics | BiocGenerics | 0.30.0 | 0.30.0 | /usr/local/lib/R/3.6/site-library/BiocGenerics | /usr/local/lib/R/3.6/site-library/BiocGenerics | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| BiocParallel | BiocParallel | 1.18.1 | 1.18.1 | /usr/local/lib/R/3.6/site-library/BiocParallel | /usr/local/lib/R/3.6/site-library/BiocParallel | TRUE | FALSE | 2019-08-06 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| biomaRt | biomaRt | 2.40.5 | 2.40.5 | /usr/local/lib/R/3.6/site-library/biomaRt | /usr/local/lib/R/3.6/site-library/biomaRt | TRUE | FALSE | 2019-10-01 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| bit | bit | 1.1.15.2 | 1.1-15.2 | /usr/local/lib/R/3.6/site-library/bit | /usr/local/lib/R/3.6/site-library/bit | FALSE | FALSE | 2020-02-10 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| bit64 | bit64 | 0.9.7 | 0.9-7 | /usr/local/lib/R/3.6/site-library/bit64 | /usr/local/lib/R/3.6/site-library/bit64 | FALSE | FALSE | 2017-05-08 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| bitops | bitops | 1.0.6 | 1.0-6 | /usr/local/lib/R/3.6/site-library/bitops | /usr/local/lib/R/3.6/site-library/bitops | FALSE | FALSE | 2013-08-17 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| blob | blob | 1.2.1 | 1.2.1 | /usr/local/lib/R/3.6/site-library/blob | /usr/local/lib/R/3.6/site-library/blob | FALSE | FALSE | 2020-01-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| bvenn | bvenn | 0.1 | 0.1 | /usr/local/lib/R/3.6/site-library/bvenn | /usr/local/lib/R/3.6/site-library/bvenn | TRUE | FALSE | 2012-08-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Cairo | Cairo | 1.5.12 | 1.5-12 | /usr/local/lib/R/3.6/site-library/Cairo | /usr/local/lib/R/3.6/site-library/Cairo | FALSE | FALSE | 2020-04-11 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| callr | callr | 3.4.3 | 3.4.3 | /usr/local/lib/R/3.6/site-library/callr | /usr/local/lib/R/3.6/site-library/callr | FALSE | FALSE | 2020-03-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| cellranger | cellranger | 1.1.0 | 1.1.0 | /usr/local/lib/R/3.6/site-library/cellranger | /usr/local/lib/R/3.6/site-library/cellranger | FALSE | FALSE | 2016-07-27 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| checkmate | checkmate | 2.0.0 | 2.0.0 | /usr/local/lib/R/3.6/site-library/checkmate | /usr/local/lib/R/3.6/site-library/checkmate | FALSE | FALSE | 2020-02-06 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| cli | cli | 2.0.2 | 2.0.2 | /usr/local/lib/R/3.6/site-library/cli | /usr/local/lib/R/3.6/site-library/cli | FALSE | FALSE | 2020-02-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| cluster | cluster | 2.1.0 | 2.1.0 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/cluster | /usr/local/Cellar/r/3.6.0_3/lib/R/library/cluster | FALSE | FALSE | 2019-06-19 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| colorspace | colorspace | 1.4.1 | 1.4-1 | /usr/local/lib/R/3.6/site-library/colorspace | /usr/local/lib/R/3.6/site-library/colorspace | FALSE | FALSE | 2019-03-18 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| crayon | crayon | 1.3.4 | 1.3.4 | /usr/local/lib/R/3.6/site-library/crayon | /usr/local/lib/R/3.6/site-library/crayon | FALSE | FALSE | 2017-09-16 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| crosstalk | crosstalk | 1.1.0.1 | 1.1.0.1 | /usr/local/lib/R/3.6/site-library/crosstalk | /usr/local/lib/R/3.6/site-library/crosstalk | FALSE | FALSE | 2020-03-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| data.table | data.table | 1.12.8 | 1.12.8 | /usr/local/lib/R/3.6/site-library/data.table | /usr/local/lib/R/3.6/site-library/data.table | FALSE | FALSE | 2019-12-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| DBI | DBI | 1.1.0 | 1.1.0 | /usr/local/lib/R/3.6/site-library/DBI | /usr/local/lib/R/3.6/site-library/DBI | FALSE | FALSE | 2019-12-15 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| DelayedArray | DelayedArray | 0.10.0 | 0.10.0 | /usr/local/lib/R/3.6/site-library/DelayedArray | /usr/local/lib/R/3.6/site-library/DelayedArray | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| desc | desc | 1.2.0 | 1.2.0 | /usr/local/lib/R/3.6/site-library/desc | /usr/local/lib/R/3.6/site-library/desc | FALSE | FALSE | 2018-05-01 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| DESeq2 | DESeq2 | 1.24.0 | 1.24.0 | /usr/local/lib/R/3.6/site-library/DESeq2 | /usr/local/lib/R/3.6/site-library/DESeq2 | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| devtools | devtools | 2.3.0 | 2.3.0 | /usr/local/lib/R/3.6/site-library/devtools | /usr/local/lib/R/3.6/site-library/devtools | FALSE | FALSE | 2020-04-10 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| digest | digest | 0.6.25 | 0.6.25 | /usr/local/lib/R/3.6/site-library/digest | /usr/local/lib/R/3.6/site-library/digest | FALSE | FALSE | 2020-02-23 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| dplyr | dplyr | 0.8.5 | 0.8.5 | /usr/local/lib/R/3.6/site-library/dplyr | /usr/local/lib/R/3.6/site-library/dplyr | TRUE | FALSE | 2020-03-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| DT | DT | 0.13 | 0.13 | /usr/local/lib/R/3.6/site-library/DT | /usr/local/lib/R/3.6/site-library/DT | TRUE | FALSE | 2020-03-23 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| ellipsis | ellipsis | 0.3.0 | 0.3.0 | /usr/local/lib/R/3.6/site-library/ellipsis | /usr/local/lib/R/3.6/site-library/ellipsis | FALSE | FALSE | 2019-09-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| evaluate | evaluate | 0.14 | 0.14 | /usr/local/lib/R/3.6/site-library/evaluate | /usr/local/lib/R/3.6/site-library/evaluate | FALSE | FALSE | 2019-05-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| fansi | fansi | 0.4.1 | 0.4.1 | /usr/local/lib/R/3.6/site-library/fansi | /usr/local/lib/R/3.6/site-library/fansi | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| farver | farver | 2.0.3 | 2.0.3 | /usr/local/lib/R/3.6/site-library/farver | /usr/local/lib/R/3.6/site-library/farver | FALSE | FALSE | 2020-01-16 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| fastmatch | fastmatch | 1.1.0 | 1.1-0 | /usr/local/lib/R/3.6/site-library/fastmatch | /usr/local/lib/R/3.6/site-library/fastmatch | FALSE | FALSE | 2017-01-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| fgsea | fgsea | 1.10.1 | 1.10.1 | /usr/local/lib/R/3.6/site-library/fgsea | /usr/local/lib/R/3.6/site-library/fgsea | TRUE | FALSE | 2019-08-21 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| foreign | foreign | 0.8.76 | 0.8-76 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/foreign | /usr/local/Cellar/r/3.6.0_3/lib/R/library/foreign | FALSE | FALSE | 2020-03-03 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| Formula | Formula | 1.2.3 | 1.2-3 | /usr/local/lib/R/3.6/site-library/Formula | /usr/local/lib/R/3.6/site-library/Formula | FALSE | FALSE | 2018-05-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| fs | fs | 1.4.1 | 1.4.1 | /usr/local/lib/R/3.6/site-library/fs | /usr/local/lib/R/3.6/site-library/fs | FALSE | FALSE | 2020-04-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| genefilter | genefilter | 1.66.0 | 1.66.0 | /usr/local/lib/R/3.6/site-library/genefilter | /usr/local/lib/R/3.6/site-library/genefilter | FALSE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| geneplotter | geneplotter | 1.62.0 | 1.62.0 | /usr/local/lib/R/3.6/site-library/geneplotter | /usr/local/lib/R/3.6/site-library/geneplotter | FALSE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| GenomeInfoDb | GenomeInfoDb | 1.20.0 | 1.20.0 | /usr/local/lib/R/3.6/site-library/GenomeInfoDb | /usr/local/lib/R/3.6/site-library/GenomeInfoDb | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| GenomeInfoDbData | GenomeInfoDbData | 1.2.1 | 1.2.1 | /usr/local/lib/R/3.6/site-library/GenomeInfoDbData | /usr/local/lib/R/3.6/site-library/GenomeInfoDbData | FALSE | FALSE | 2019-07-01 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| GenomicRanges | GenomicRanges | 1.36.1 | 1.36.1 | /usr/local/lib/R/3.6/site-library/GenomicRanges | /usr/local/lib/R/3.6/site-library/GenomicRanges | TRUE | FALSE | 2019-09-06 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| ggplot2 | ggplot2 | 3.3.0 | 3.3.0 | /usr/local/lib/R/3.6/site-library/ggplot2 | /usr/local/lib/R/3.6/site-library/ggplot2 | TRUE | FALSE | 2020-03-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| glue | glue | 1.4.0 | 1.4.0 | /usr/local/lib/R/3.6/site-library/glue | /usr/local/lib/R/3.6/site-library/glue | FALSE | FALSE | 2020-04-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| graph | graph | 1.62.0 | 1.62.0 | /usr/local/lib/R/3.6/site-library/graph | /usr/local/lib/R/3.6/site-library/graph | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| gridExtra | gridExtra | 2.3 | 2.3 | /usr/local/lib/R/3.6/site-library/gridExtra | /usr/local/lib/R/3.6/site-library/gridExtra | FALSE | FALSE | 2017-09-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| GSEABase | GSEABase | 1.46.0 | 1.46.0 | /usr/local/lib/R/3.6/site-library/GSEABase | /usr/local/lib/R/3.6/site-library/GSEABase | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| gtable | gtable | 0.3.0 | 0.3.0 | /usr/local/lib/R/3.6/site-library/gtable | /usr/local/lib/R/3.6/site-library/gtable | FALSE | FALSE | 2019-03-25 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Hmisc | Hmisc | 4.4.0 | 4.4-0 | /usr/local/lib/R/3.6/site-library/Hmisc | /usr/local/lib/R/3.6/site-library/Hmisc | FALSE | FALSE | 2020-03-23 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| hms | hms | 0.5.3 | 0.5.3 | /usr/local/lib/R/3.6/site-library/hms | /usr/local/lib/R/3.6/site-library/hms | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| htmlTable | htmlTable | 1.13.3 | 1.13.3 | /usr/local/lib/R/3.6/site-library/htmlTable | /usr/local/lib/R/3.6/site-library/htmlTable | FALSE | FALSE | 2019-12-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| htmltools | htmltools | 0.4.0 | 0.4.0 | /usr/local/lib/R/3.6/site-library/htmltools | /usr/local/lib/R/3.6/site-library/htmltools | FALSE | FALSE | 2019-10-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| htmlwidgets | htmlwidgets | 1.5.1 | 1.5.1 | /usr/local/lib/R/3.6/site-library/htmlwidgets | /usr/local/lib/R/3.6/site-library/htmlwidgets | FALSE | FALSE | 2019-10-08 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| httr | httr | 1.4.1 | 1.4.1 | /usr/local/lib/R/3.6/site-library/httr | /usr/local/lib/R/3.6/site-library/httr | FALSE | FALSE | 2019-08-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| IRanges | IRanges | 2.18.3 | 2.18.3 | /usr/local/lib/R/3.6/site-library/IRanges | /usr/local/lib/R/3.6/site-library/IRanges | TRUE | FALSE | 2019-09-24 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| jpeg | jpeg | 0.1.8.1 | 0.1-8.1 | /usr/local/lib/R/3.6/site-library/jpeg | /usr/local/lib/R/3.6/site-library/jpeg | FALSE | FALSE | 2019-10-24 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| jsonlite | jsonlite | 1.6.1 | 1.6.1 | /usr/local/lib/R/3.6/site-library/jsonlite | /usr/local/lib/R/3.6/site-library/jsonlite | FALSE | FALSE | 2020-02-02 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| knitr | knitr | 1.28 | 1.28 | /usr/local/lib/R/3.6/site-library/knitr | /usr/local/lib/R/3.6/site-library/knitr | FALSE | FALSE | 2020-02-06 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| labeling | labeling | 0.3 | 0.3 | /usr/local/lib/R/3.6/site-library/labeling | /usr/local/lib/R/3.6/site-library/labeling | FALSE | FALSE | 2014-08-23 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| lattice | lattice | 0.20.41 | 0.20-41 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/lattice | /usr/local/Cellar/r/3.6.0_3/lib/R/library/lattice | FALSE | FALSE | 2020-04-02 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| latticeExtra | latticeExtra | 0.6.29 | 0.6-29 | /usr/local/lib/R/3.6/site-library/latticeExtra | /usr/local/lib/R/3.6/site-library/latticeExtra | FALSE | FALSE | 2019-12-19 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| lazyeval | lazyeval | 0.2.2 | 0.2.2 | /usr/local/lib/R/3.6/site-library/lazyeval | /usr/local/lib/R/3.6/site-library/lazyeval | FALSE | FALSE | 2019-03-15 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| lifecycle | lifecycle | 0.2.0 | 0.2.0 | /usr/local/lib/R/3.6/site-library/lifecycle | /usr/local/lib/R/3.6/site-library/lifecycle | FALSE | FALSE | 2020-03-06 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| locfit | locfit | 1.5.9.4 | 1.5-9.4 | /usr/local/lib/R/3.6/site-library/locfit | /usr/local/lib/R/3.6/site-library/locfit | FALSE | FALSE | 2020-03-25 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| magrittr | magrittr | 1.5 | 1.5 | /usr/local/lib/R/3.6/site-library/magrittr | /usr/local/lib/R/3.6/site-library/magrittr | TRUE | FALSE | 2014-11-22 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Matrix | Matrix | 1.2.18 | 1.2-18 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/Matrix | /usr/local/Cellar/r/3.6.0_3/lib/R/library/Matrix | FALSE | FALSE | 2019-11-27 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| matrixStats | matrixStats | 0.56.0 | 0.56.0 | /usr/local/lib/R/3.6/site-library/matrixStats | /usr/local/lib/R/3.6/site-library/matrixStats | TRUE | FALSE | 2020-03-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| memoise | memoise | 1.1.0 | 1.1.0 | /usr/local/lib/R/3.6/site-library/memoise | /usr/local/lib/R/3.6/site-library/memoise | FALSE | FALSE | 2017-04-21 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| munsell | munsell | 0.5.0 | 0.5.0 | /usr/local/lib/R/3.6/site-library/munsell | /usr/local/lib/R/3.6/site-library/munsell | FALSE | FALSE | 2018-06-12 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| network | network | 1.16.0 | 1.16.0 | /usr/local/lib/R/3.6/site-library/network | /usr/local/lib/R/3.6/site-library/network | TRUE | FALSE | 2019-12-01 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| nnet | nnet | 7.3.13 | 7.3-13 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/nnet | /usr/local/Cellar/r/3.6.0_3/lib/R/library/nnet | FALSE | FALSE | 2020-02-25 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| pander | pander | 0.6.3 | 0.6.3 | /usr/local/lib/R/3.6/site-library/pander | /usr/local/lib/R/3.6/site-library/pander | TRUE | FALSE | 2018-11-06 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pheatmap | pheatmap | 1.0.12 | 1.0.12 | /usr/local/lib/R/3.6/site-library/pheatmap | /usr/local/lib/R/3.6/site-library/pheatmap | TRUE | FALSE | 2019-01-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pillar | pillar | 1.4.4 | 1.4.4 | /usr/local/lib/R/3.6/site-library/pillar | /usr/local/lib/R/3.6/site-library/pillar | FALSE | FALSE | 2020-05-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pkgbuild | pkgbuild | 1.0.8 | 1.0.8 | /usr/local/lib/R/3.6/site-library/pkgbuild | /usr/local/lib/R/3.6/site-library/pkgbuild | FALSE | FALSE | 2020-05-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pkgconfig | pkgconfig | 2.0.3 | 2.0.3 | /usr/local/lib/R/3.6/site-library/pkgconfig | /usr/local/lib/R/3.6/site-library/pkgconfig | FALSE | FALSE | 2019-09-22 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pkgload | pkgload | 1.0.2 | 1.0.2 | /usr/local/lib/R/3.6/site-library/pkgload | /usr/local/lib/R/3.6/site-library/pkgload | FALSE | FALSE | 2018-10-29 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| plotly | plotly | 4.9.2.1 | 4.9.2.1 | /usr/local/lib/R/3.6/site-library/plotly | /usr/local/lib/R/3.6/site-library/plotly | TRUE | FALSE | 2020-04-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| plyr | plyr | 1.8.6 | 1.8.6 | /usr/local/lib/R/3.6/site-library/plyr | /usr/local/lib/R/3.6/site-library/plyr | TRUE | FALSE | 2020-03-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| png | png | 0.1.7 | 0.1-7 | /usr/local/lib/R/3.6/site-library/png | /usr/local/lib/R/3.6/site-library/png | FALSE | FALSE | 2013-12-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| prettyunits | prettyunits | 1.1.1 | 1.1.1 | /usr/local/lib/R/3.6/site-library/prettyunits | /usr/local/lib/R/3.6/site-library/prettyunits | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| processx | processx | 3.4.2 | 3.4.2 | /usr/local/lib/R/3.6/site-library/processx | /usr/local/lib/R/3.6/site-library/processx | FALSE | FALSE | 2020-02-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| progress | progress | 1.2.2 | 1.2.2 | /usr/local/lib/R/3.6/site-library/progress | /usr/local/lib/R/3.6/site-library/progress | FALSE | FALSE | 2019-05-16 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| ps | ps | 1.3.2 | 1.3.2 | /usr/local/lib/R/3.6/site-library/ps | /usr/local/lib/R/3.6/site-library/ps | FALSE | FALSE | 2020-02-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| purrr | purrr | 0.3.4 | 0.3.4 | /usr/local/lib/R/3.6/site-library/purrr | /usr/local/lib/R/3.6/site-library/purrr | FALSE | FALSE | 2020-04-17 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| R6 | R6 | 2.4.1 | 2.4.1 | /usr/local/lib/R/3.6/site-library/R6 | /usr/local/lib/R/3.6/site-library/R6 | FALSE | FALSE | 2019-11-12 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| RColorBrewer | RColorBrewer | 1.1.2 | 1.1-2 | /usr/local/lib/R/3.6/site-library/RColorBrewer | /usr/local/lib/R/3.6/site-library/RColorBrewer | FALSE | FALSE | 2014-12-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Rcpp | Rcpp | 1.0.4.6 | 1.0.4.6 | /usr/local/lib/R/3.6/site-library/Rcpp | /usr/local/lib/R/3.6/site-library/Rcpp | TRUE | FALSE | 2020-04-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| RCurl | RCurl | 1.98.1.2 | 1.98-1.2 | /usr/local/lib/R/3.6/site-library/RCurl | /usr/local/lib/R/3.6/site-library/RCurl | FALSE | FALSE | 2020-04-18 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| readxl | readxl | 1.3.1 | 1.3.1 | /usr/local/lib/R/3.6/site-library/readxl | /usr/local/lib/R/3.6/site-library/readxl | TRUE | FALSE | 2019-03-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| remotes | remotes | 2.1.1 | 2.1.1 | /usr/local/lib/R/3.6/site-library/remotes | /usr/local/lib/R/3.6/site-library/remotes | FALSE | FALSE | 2020-02-15 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| reshape2 | reshape2 | 1.4.4 | 1.4.4 | /usr/local/lib/R/3.6/site-library/reshape2 | /usr/local/lib/R/3.6/site-library/reshape2 | TRUE | FALSE | 2020-04-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| rlang | rlang | 0.4.6 | 0.4.6 | /usr/local/lib/R/3.6/site-library/rlang | /usr/local/lib/R/3.6/site-library/rlang | FALSE | FALSE | 2020-05-02 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| rmarkdown | rmarkdown | 2.1 | 2.1 | /usr/local/lib/R/3.6/site-library/rmarkdown | /usr/local/lib/R/3.6/site-library/rmarkdown | FALSE | FALSE | 2020-01-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| rpart | rpart | 4.1.15 | 4.1-15 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/rpart | /usr/local/Cellar/r/3.6.0_3/lib/R/library/rpart | FALSE | FALSE | 2019-04-12 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| rprojroot | rprojroot | 1.3.2 | 1.3-2 | /usr/local/lib/R/3.6/site-library/rprojroot | /usr/local/lib/R/3.6/site-library/rprojroot | FALSE | FALSE | 2018-01-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| RSQLite | RSQLite | 2.2.0 | 2.2.0 | /usr/local/lib/R/3.6/site-library/RSQLite | /usr/local/lib/R/3.6/site-library/RSQLite | FALSE | FALSE | 2020-01-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| rstudioapi | rstudioapi | 0.11 | 0.11 | /usr/local/lib/R/3.6/site-library/rstudioapi | /usr/local/lib/R/3.6/site-library/rstudioapi | FALSE | FALSE | 2020-02-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| S4Vectors | S4Vectors | 0.22.1 | 0.22.1 | /usr/local/lib/R/3.6/site-library/S4Vectors | /usr/local/lib/R/3.6/site-library/S4Vectors | TRUE | FALSE | 2019-09-09 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| scales | scales | 1.1.0 | 1.1.0 | /usr/local/lib/R/3.6/site-library/scales | /usr/local/lib/R/3.6/site-library/scales | FALSE | FALSE | 2019-11-18 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| sessioninfo | sessioninfo | 1.1.1 | 1.1.1 | /usr/local/lib/R/3.6/site-library/sessioninfo | /usr/local/lib/R/3.6/site-library/sessioninfo | FALSE | FALSE | 2018-11-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| stringi | stringi | 1.4.6 | 1.4.6 | /usr/local/lib/R/3.6/site-library/stringi | /usr/local/lib/R/3.6/site-library/stringi | FALSE | FALSE | 2020-02-17 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| stringr | stringr | 1.4.0 | 1.4.0 | /usr/local/lib/R/3.6/site-library/stringr | /usr/local/lib/R/3.6/site-library/stringr | FALSE | FALSE | 2019-02-10 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| SummarizedExperiment | SummarizedExperiment | 1.14.1 | 1.14.1 | /usr/local/lib/R/3.6/site-library/SummarizedExperiment | /usr/local/lib/R/3.6/site-library/SummarizedExperiment | TRUE | FALSE | 2019-07-31 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| survival | survival | 3.1.12 | 3.1-12 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/survival | /usr/local/Cellar/r/3.6.0_3/lib/R/library/survival | FALSE | FALSE | 2020-04-10 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| testthat | testthat | 2.3.2 | 2.3.2 | /usr/local/lib/R/3.6/site-library/testthat | /usr/local/lib/R/3.6/site-library/testthat | FALSE | FALSE | 2020-03-02 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| tibble | tibble | 3.0.1 | 3.0.1 | /usr/local/lib/R/3.6/site-library/tibble | /usr/local/lib/R/3.6/site-library/tibble | FALSE | FALSE | 2020-04-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| tidyr | tidyr | 1.0.2 | 1.0.2 | /usr/local/lib/R/3.6/site-library/tidyr | /usr/local/lib/R/3.6/site-library/tidyr | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| tidyselect | tidyselect | 1.0.0 | 1.0.0 | /usr/local/lib/R/3.6/site-library/tidyselect | /usr/local/lib/R/3.6/site-library/tidyselect | FALSE | FALSE | 2020-01-27 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| usethis | usethis | 1.6.0 | 1.6.0 | /usr/local/lib/R/3.6/site-library/usethis | /usr/local/lib/R/3.6/site-library/usethis | FALSE | FALSE | 2020-04-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| vctrs | vctrs | 0.2.4 | 0.2.4 | /usr/local/lib/R/3.6/site-library/vctrs | /usr/local/lib/R/3.6/site-library/vctrs | FALSE | FALSE | 2020-03-10 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| viridisLite | viridisLite | 0.3.0 | 0.3.0 | /usr/local/lib/R/3.6/site-library/viridisLite | /usr/local/lib/R/3.6/site-library/viridisLite | FALSE | FALSE | 2018-02-01 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| withr | withr | 2.2.0 | 2.2.0 | /usr/local/lib/R/3.6/site-library/withr | /usr/local/lib/R/3.6/site-library/withr | FALSE | FALSE | 2020-04-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| xfun | xfun | 0.13 | 0.13 | /usr/local/lib/R/3.6/site-library/xfun | /usr/local/lib/R/3.6/site-library/xfun | FALSE | FALSE | 2020-04-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| XML | XML | 3.99.0.3 | 3.99-0.3 | /usr/local/lib/R/3.6/site-library/XML | /usr/local/lib/R/3.6/site-library/XML | TRUE | FALSE | 2020-01-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| xtable | xtable | 1.8.4 | 1.8-4 | /usr/local/lib/R/3.6/site-library/xtable | /usr/local/lib/R/3.6/site-library/xtable | FALSE | FALSE | 2019-04-21 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| XVector | XVector | 0.24.0 | 0.24.0 | /usr/local/lib/R/3.6/site-library/XVector | /usr/local/lib/R/3.6/site-library/XVector | FALSE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| yaml | yaml | 2.2.1 | 2.2.1 | /usr/local/lib/R/3.6/site-library/yaml | /usr/local/lib/R/3.6/site-library/yaml | FALSE | FALSE | 2020-02-01 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| zlibbioc | zlibbioc | 1.30.0 | 1.30.0 | /usr/local/lib/R/3.6/site-library/zlibbioc | /usr/local/lib/R/3.6/site-library/zlibbioc | FALSE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |